Contacts of the strand formed by residues 164 - 173 (chain A) in PDB entry 4Y1W


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with LEU 164 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  TRP*     4.0    24.9    -      -       +      +
    121A  VAL*     3.4     7.0    -      -       -      +
    122A  LYS*     3.8    36.8    -      -       +      +
    157A  HIS*     3.5    26.9    +      -       +      -
    158A  PRO*     4.1    33.4    -      -       +      +
    160A  SER*     3.9    22.2    -      -       -      +
    162A  GLN      3.3    11.3    +      -       -      +
    163A  ARG*     1.3    76.2    -      -       -      +
    165A  LYS*     1.3    72.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  TRP*     3.4     7.6    -      -       -      -
    121A  VAL      2.8    32.8    +      -       -      +
    123A  LEU*     4.0    36.1    -      -       +      -
    126A  LEU*     4.3    18.6    -      -       +      -
    163A  ARG*     3.7    28.2    -      -       -      +
    164A  LEU*     1.3    85.5    -      -       -      +
    166A  ARG*     1.3    67.1    +      -       -      +
    167A  VAL*     3.4     5.3    +      -       +      +
    212A  THR*     5.0     6.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  THR      3.8     3.4    -      -       -      -
    120A  TRP*     3.4    24.3    -      -       +      -
    151A  LYS*     2.5    40.6    +      -       -      +
    154A  SER*     2.2    57.2    +      -       -      +
    155A  VAL*     3.6    14.3    -      -       -      +
    165A  LYS*     1.3    72.5    -      -       -      +
    167A  VAL*     1.3    65.1    +      -       -      +
    168A  LEU*     3.9    24.0    -      -       +      +
    211A  HIS*     5.4     0.9    -      -       -      -
    212A  THR*     3.8    19.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  ARG      4.0     0.3    -      -       -      +
    118A  GLY*     3.3     3.5    -      -       -      -
    119A  THR      2.9    37.5    +      -       -      +
    121A  VAL*     3.6    28.9    -      -       +      -
    126A  LEU*     4.9     5.2    -      -       +      -
    165A  LYS*     3.7     9.9    -      -       +      +
    166A  ARG*     1.3    80.1    -      -       -      +
    168A  LEU*     1.3    69.1    +      -       -      +
    169A  PHE*     3.6    29.7    +      -       +      -
    212A  THR*     3.5    23.1    -      -       +      +
    214A  ILE*     3.8    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  ILE*     3.4    36.5    -      -       +      +
    117A  ARG      3.6     2.7    -      -       -      +
    118A  GLY*     3.8     8.5    -      -       -      -
    150A  ALA*     4.7     2.0    -      -       +      +
    151A  LYS*     4.2    24.9    -      -       +      +
    154A  SER*     3.7    21.1    -      -       -      +
    166A  ARG*     3.9    23.3    -      -       +      +
    167A  VAL*     1.3    82.1    -      -       -      +
    169A  PHE*     1.3    62.2    +      -       -      +
    170A  GLU      4.1     0.3    +      -       -      -
    212A  THR      3.1     6.7    +      -       -      -
    213A  TYR*     3.3    28.2    -      -       +      +
    214A  ILE      3.0    23.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  ILE*     4.6     1.5    -      -       -      +
    116A  TYR*     3.3    13.0    -      -       -      +
    117A  ARG*     2.8    50.8    +      -       +      +
    119A  THR*     3.7    26.2    -      -       +      -
    121A  VAL*     4.6     2.0    -      -       +      -
    135A  LEU*     3.7    30.5    -      -       +      -
    167A  VAL*     3.6    26.0    -      -       +      -
    168A  LEU*     1.3    73.6    -      -       -      +
    170A  GLU*     1.3    59.5    +      -       -      +
    171A  VAL*     3.9    16.7    +      -       +      +
    214A  ILE*     3.2    34.5    -      -       +      -
    216A  VAL*     3.9    15.0    -      -       +      -
    232A  LEU*     4.2    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  PHE*     3.8    47.7    +      -       +      -
     22A  ASP      5.0     0.2    +      -       -      -
     23A  ALA*     4.1     8.5    +      -       -      +
     24A  ILE*     4.2     3.1    -      -       +      +
    114A  THR*     3.8    15.2    -      -       +      +
    115A  ALA      3.7     2.9    -      -       -      -
    116A  TYR*     3.0    37.7    +      -       +      -
    168A  LEU      4.1     1.0    +      -       -      -
    169A  PHE*     1.3    71.6    -      -       -      +
    171A  VAL*     1.3    59.7    +      -       -      +
    172A  LYS      3.9     0.5    +      -       -      -
    214A  ILE      3.0     6.5    +      -       -      -
    215A  GLY*     3.3     3.7    -      -       -      -
    216A  VAL      3.0    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  THR*     3.3     6.9    -      -       -      -
    115A  ALA*     2.8    50.1    +      -       +      +
    116A  TYR*     4.8     1.1    -      -       -      +
    117A  ARG*     4.9     3.4    -      -       +      +
    141A  THR*     6.3     0.4    -      -       +      -
    143A  THR*     4.4    15.3    -      -       +      -
    169A  PHE*     4.1    16.8    -      -       +      +
    170A  GLU*     1.3    73.8    -      -       -      +
    172A  LYS*     1.3    66.4    +      -       -      +
    173A  ILE*     3.5    24.6    +      -       +      +
    194A  PHE*     4.9     0.9    -      -       +      -
    200A  PHE*     3.9    27.8    -      -       +      -
    216A  VAL*     3.4    19.7    -      -       +      -
    218A  THR*     4.4     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  LYS*     5.0     1.8    -      -       -      +
    113A  GLY*     3.7    18.8    -      -       -      +
    114A  THR*     4.5     9.4    -      -       -      +
    170A  GLU*     3.9     1.2    +      -       -      +
    171A  VAL*     1.3    70.6    -      -       -      +
    173A  ILE*     1.3    85.9    +      -       -      +
    174A  ASN*     3.8    19.2    +      -       -      +
    216A  VAL      2.8    16.7    +      -       -      +
    217A  GLU*     3.3    14.1    -      -       +      +
    218A  THR*     3.0    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  TYR*     3.2    29.8    -      -       +      +
    112A  LYS*     3.2     4.7    -      -       -      -
    113A  GLY      2.7    36.6    +      -       -      +
    115A  ALA*     3.8    26.5    -      -       +      -
    143A  THR*     4.2     0.9    -      -       -      +
    171A  VAL*     3.7    22.0    -      -       +      +
    172A  LYS*     1.3    78.3    +      -       -      +
    174A  ASN*     1.3    60.9    +      -       -      +
    175A  GLN      3.6    20.2    -      -       -      +
    177A  GLY*     4.1     4.0    -      -       -      +
    192A  VAL*     4.0    15.3    -      -       +      -
    194A  PHE*     3.7    28.0    -      -       +      -
    218A  THR*     3.7     3.1    -      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il